Correlations (Clean code)
Eva Kim
12/06/2024
Taking the intersection of differentially abundant taxa and graphing them revealed that even when taking the intersection, lung tissue taxa prevalence was spurious. Since DAA was redone to reflect testing based on hypotheses, I am rerunning this code to see if there are differences. Lung tissue taxa prevalence is still spurious so I will be focusing on fecal taxa only.
1 Method
One method of running correlations is using the transformed relative abundance data then using Pearson correlation. I had previously used arcsine transformation and considered the centered-log ratio (CLR) transformation. However, plotting correlations with raw relative abundance may show non-obvious relationships. Per Dr. Shi’s recommendation, I will be using Spearman’s rank correlation (non-parametric) with the raw relative abundance values instead.
There are certain lung tissue taxa of interest for Dr. Ingram: Flavobacteriales, Capnocytophaga and Flavobacterium. In addition, differential immune cell counting data has been added on 2/10/2024.
2 Set-Up
2.1 Load libraries and directories
# rm(list = ls(all = TRUE)) ## Unload all packages if necessary
library(rstatix)
library(ggpubr)
library(pals)
library(RColorBrewer)
library(ggrepel)
library(DT)
library(plotly)
library(parallel)
library(dplyr)
library(tidyr)
library(readr)
library(tibble)
library(stringr)
library(phyloseq)
library(Hmisc)
library(cowplot)
library(ggtext)rm(list=ls()) # clear environment
git.dir = file.path("/hpc/group/dmc/Eva/GLP_KO_Microbiome_final") # CHANGE ME
fig.dir = file.path(git.dir, "figures")
map.file = file.path(git.dir, "Metadata_GLP1.csv")
meta.df = read_csv(map.file, show_col_types = FALSE)
F_hfd_intersect.file = file.path(git.dir, "fecal_deseq_hfd_intersect.csv")
f.hfd.intersect = read_csv(F_hfd_intersect.file, show_col_types = FALSE)
F_nosurgery_intersect.file = file.path(git.dir, "fecal_deseq_nosurgery_intersect.csv")
f.nosurgery.intersect = read_csv(F_nosurgery_intersect.file, show_col_types = FALSE)
F_RA.file = file.path("fecal_relative_abundance.csv")
f.ra = read_csv(F_RA.file, show_col_types = FALSE)
diff.file = file.path(git.dir, "GLP1_study_balf_diff_counts.csv")
diff.df = read_csv(diff.file,col_names = TRUE, show_col_types = FALSE )
glucose.file = file.path(git.dir, "GLP1_study_glucose_calculations.csv")
glucose.df = read_csv(glucose.file, col_names = TRUE, show_col_types = FALSE )
protein.file = file.path(git.dir, "GLP1_study_proteins.csv")
protein.df = read_csv(protein.file,col_names = TRUE, show_col_types = FALSE )
trichrome.file = file.path(git.dir, "GLP1_study_trichrome.csv")
trichrome.df = read_csv(trichrome.file,col_names = TRUE, show_col_types = FALSE )
hist.file = file.path(git.dir, "GLP1_study_histology.csv")
hist.df = read_csv(hist.file, show_col_types = FALSE)3 Correlations: Tests to run
Based on the graphs of differentially abundant taxa that were both identified by DESeq2 and ANCOM-II, many taxa were spurious. As such, I will only run taxon-health marker correlation with fecal taxa.
In addition, there are a lot of variables to choose from and I expect more information to be available in near future. For now, the variables that I am most interested are: 1. Weight 2. Glucose calculations: AUC, MaxPeak, baseline 3. Serum protein levels except for insulin 4. Immune cells (eosinophils and neutrophils) 5. Histology scores and trichrome data
For simplicity, only fecal microbiome relative abundance on the same day as the health data was collected will be used.
3.1 Clean up metadata for correlations
meta.df %>%
filter(Sample_type == "Fecal" & Type == "True Sample") %>%
select(Label, Mouse, Genotype:Surgery, Week, contains("Weight")) -> meta.slim
glucose.df %>% select(Mouse, Week, AUC:Glucose_min_0) -> glucose.slim
meta.slim %>%
left_join(glucose.slim, by = c("Mouse", "Week")) %>% filter(is.na(Mouse) == FALSE) -> corr.df
meta.slim %>% filter(Week == 13) %>%
right_join(diff.df, by = "Mouse") -> diff.meta.dfhead(corr.df)head(diff.meta.df)meta.slim %>% dim()## [1] 182 12f.ra %>% distinct(Sample) %>% nrow()## [1] 1783.2 Subset fecal taxa to only those that were differentially abundant
f.hfd.intersect$Group <- "HFD"
f.nosurgery.intersect$Group <- "No Surgery"
rbind(f.hfd.intersect, f.nosurgery.intersect) -> f.intersect
f.intersectf.ra %>% filter(OTU %in% f.intersect$row) %>%
select(Label, OTU, Abundance) %>%
pivot_wider(names_from = OTU,
values_from = Abundance) %>%
dplyr::mutate(Label = as.character(Label)) -> FullRA.df
FullRA.df %>% head()3.3 Weight Correlations
corr.df %>% select(Label, Week, Weight_g_wk0:Weight_g_wk13) %>%
mutate(Weight = case_when(Week == 0 ~ Weight_g_wk0,
Week == 10 ~ Weight_g_wk10,
Week == 13 ~ Weight_g_wk13)) %>%
select(Label, Weight) %>%
filter(is.na(Weight) != TRUE) %>%
left_join(FullRA.df, by = "Label") -> Weight.corr.df
head(Weight.corr.df)dim(Weight.corr.df)## [1] 178 43This dataframe structure is such that the recorded weight matches the fecal sample label for the day it was collected.
Weight.corr.df %>% colnames()## [1] "Label"
## [2] "Weight"
## [3] "Bifidobacterium"
## [4] "Romboutsia"
## [5] "Lactococcus"
## [6] "Rikenella"
## [7] "Prevotellaceae UCG-001"
## [8] "Rikenellaceae RC9 gut group"
## [9] "Coriobacteriaceae UCG-002"
## [10] "Prevotellaceae NK3B31 group"
## [11] "Tyzzerella"
## [12] "Parasutterella"
## [13] "Lachnospiraceae UCG-001"
## [14] "Muribaculum"
## [15] "Tuzzerella"
## [16] "Candidatus Arthromitus"
## [17] "Acetatifactor"
## [18] "Marvinbryantia"
## [19] "Butyricicoccus"
## [20] "Candidatus Stoquefichus"
## [21] "Lactobacillaceae"
## [22] "Bifidobacteriaceae"
## [23] "Peptostreptococcaceae"
## [24] "Streptococcaceae"
## [25] "Prevotellaceae"
## [26] "Atopobiaceae"
## [27] "Sutterellaceae"
## [28] "Enterococcaceae"
## [29] "[Eubacterium] coprostanoligenes group"
## [30] "Erysipelatoclostridiaceae"
## [31] "Lactobacillales"
## [32] "Bifidobacteriales"
## [33] "Peptostreptococcales-Tissierellales"
## [34] "Oscillospirales"
## [35] "Burkholderiales"
## [36] "Clostridia UCG-014"
## [37] "Actinobacteria"
## [38] "Coriobacteriia"
## [39] "Gammaproteobacteria"
## [40] "Verrucomicrobiae"
## [41] "Actinobacteriota"
## [42] "Proteobacteria"
## [43] "Verrucomicrobiota"corr.df %>% select(Label, Mouse, Week, Weight_g_wk0:Weight_g_wk13) %>%
mutate(Weight = case_when(Week == 0 ~ Weight_g_wk0,
Week == 10 ~ Weight_g_wk10,
Week == 13 ~ Weight_g_wk13)) %>%
distinct(Mouse) %>% nrow() -> weight.n.mouse
weight.n.mouse## [1] 90Weight.corr.df %>%
rstatix::cor_test(vars = Weight,
vars2 = c("Bifidobacterium":"Verrucomicrobiota"),
method = "spearman") -> Weight.corr.res
Weight.corr.res$n_mouse <- weight.n.mouse
Weight.corr.res$n_feces <- nrow(Weight.corr.df)
Weight.corr.res$Week <- "0, 10, 13 (aggregated)"3.4 Glucose tolerance metrics
corr.df %>% filter(is.na(AUC) != TRUE) %>%
select(Label, AUC:Glucose_min_0) %>%
left_join(FullRA.df, by = "Label") -> glucose.df
glucose.df %>% colnames()## [1] "Label"
## [2] "AUC"
## [3] "MaxPeak"
## [4] "Glucose_min_0"
## [5] "Bifidobacterium"
## [6] "Romboutsia"
## [7] "Lactococcus"
## [8] "Rikenella"
## [9] "Prevotellaceae UCG-001"
## [10] "Rikenellaceae RC9 gut group"
## [11] "Coriobacteriaceae UCG-002"
## [12] "Prevotellaceae NK3B31 group"
## [13] "Tyzzerella"
## [14] "Parasutterella"
## [15] "Lachnospiraceae UCG-001"
## [16] "Muribaculum"
## [17] "Tuzzerella"
## [18] "Candidatus Arthromitus"
## [19] "Acetatifactor"
## [20] "Marvinbryantia"
## [21] "Butyricicoccus"
## [22] "Candidatus Stoquefichus"
## [23] "Lactobacillaceae"
## [24] "Bifidobacteriaceae"
## [25] "Peptostreptococcaceae"
## [26] "Streptococcaceae"
## [27] "Prevotellaceae"
## [28] "Atopobiaceae"
## [29] "Sutterellaceae"
## [30] "Enterococcaceae"
## [31] "[Eubacterium] coprostanoligenes group"
## [32] "Erysipelatoclostridiaceae"
## [33] "Lactobacillales"
## [34] "Bifidobacteriales"
## [35] "Peptostreptococcales-Tissierellales"
## [36] "Oscillospirales"
## [37] "Burkholderiales"
## [38] "Clostridia UCG-014"
## [39] "Actinobacteria"
## [40] "Coriobacteriia"
## [41] "Gammaproteobacteria"
## [42] "Verrucomicrobiae"
## [43] "Actinobacteriota"
## [44] "Proteobacteria"
## [45] "Verrucomicrobiota"corr.df %>% filter(is.na(AUC) != TRUE) %>%
distinct(Mouse) %>% nrow() -> glucose.n.mouse
glucose.n.mouse## [1] 58glucose.df %>%
rstatix::cor_test(vars = c(AUC, MaxPeak, Glucose_min_0),
vars2 = c("Bifidobacterium":"Verrucomicrobiota"),
method = "spearman") -> glucose.corr.res
glucose.corr.res$n_mouse <- glucose.n.mouse
glucose.corr.res$n_feces <- nrow(glucose.df)
glucose.corr.res$Week <- "0, 10, 12 (aggregated)"3.5 Serum protein correlations
protein.df %>% dplyr::rename(
C_peptide_pg_ml = `C-Peptide_pg_ml`,
GLP1_pM = `GLP-1_pM`,
Insulin_uIU_ml = `Insulin_uIU/ml`
) -> protein.df
meta.slim %>%
filter(Mouse %in% protein.df$Sample) %>%
filter(Week==13) %>%
dplyr::rename(Sample = Mouse) %>%
right_join(protein.df, by = "Sample") %>%
select(Label, Sample, C_peptide_pg_ml:PYY_pg_ml) %>%
left_join(FullRA.df, by = "Label") -> protein.micro.corr
protein.micro.corr %>% colnames()## [1] "Label"
## [2] "Sample"
## [3] "C_peptide_pg_ml"
## [4] "Ghrelin_pg_ml"
## [5] "GLP1_pM"
## [6] "Insulin_uIU_ml"
## [7] "Leptin_pg_ml"
## [8] "PYY_pg_ml"
## [9] "Bifidobacterium"
## [10] "Romboutsia"
## [11] "Lactococcus"
## [12] "Rikenella"
## [13] "Prevotellaceae UCG-001"
## [14] "Rikenellaceae RC9 gut group"
## [15] "Coriobacteriaceae UCG-002"
## [16] "Prevotellaceae NK3B31 group"
## [17] "Tyzzerella"
## [18] "Parasutterella"
## [19] "Lachnospiraceae UCG-001"
## [20] "Muribaculum"
## [21] "Tuzzerella"
## [22] "Candidatus Arthromitus"
## [23] "Acetatifactor"
## [24] "Marvinbryantia"
## [25] "Butyricicoccus"
## [26] "Candidatus Stoquefichus"
## [27] "Lactobacillaceae"
## [28] "Bifidobacteriaceae"
## [29] "Peptostreptococcaceae"
## [30] "Streptococcaceae"
## [31] "Prevotellaceae"
## [32] "Atopobiaceae"
## [33] "Sutterellaceae"
## [34] "Enterococcaceae"
## [35] "[Eubacterium] coprostanoligenes group"
## [36] "Erysipelatoclostridiaceae"
## [37] "Lactobacillales"
## [38] "Bifidobacteriales"
## [39] "Peptostreptococcales-Tissierellales"
## [40] "Oscillospirales"
## [41] "Burkholderiales"
## [42] "Clostridia UCG-014"
## [43] "Actinobacteria"
## [44] "Coriobacteriia"
## [45] "Gammaproteobacteria"
## [46] "Verrucomicrobiae"
## [47] "Actinobacteriota"
## [48] "Proteobacteria"
## [49] "Verrucomicrobiota"protein.micro.corr %>%
rstatix::cor_test(vars = c(C_peptide_pg_ml:PYY_pg_ml),
vars2 = c("Bifidobacterium":"Verrucomicrobiota"),
method = "spearman") -> protein.corr.resprotein.df %>% pivot_longer(
cols = c(C_peptide_pg_ml:PYY_pg_ml),
names_to = "var1",
values_to = "value"
) %>% filter(is.na(value) == FALSE) %>%
dplyr::count(var1) %>%
dplyr::mutate(n_mouse = n,
n_feces = n) %>% dplyr::select(-n) -> protein.n
protein.nprotein.corr.res$Week <- "13"
protein.corr.res %>% left_join(protein.n, by = "var1") -> protein.corr.res
head(protein.corr.res)3.6 Immune cells
diff.meta.df %>%
dplyr::filter(Intranasal_Treatment == "HDM") %>%
select(Label, Per_Eos, Per_Neut) %>%
left_join(FullRA.df, by = "Label") %>%
filter(is.na(Label) == FALSE) -> diff.corr
diff.corr %>% colnames()## [1] "Label"
## [2] "Per_Eos"
## [3] "Per_Neut"
## [4] "Bifidobacterium"
## [5] "Romboutsia"
## [6] "Lactococcus"
## [7] "Rikenella"
## [8] "Prevotellaceae UCG-001"
## [9] "Rikenellaceae RC9 gut group"
## [10] "Coriobacteriaceae UCG-002"
## [11] "Prevotellaceae NK3B31 group"
## [12] "Tyzzerella"
## [13] "Parasutterella"
## [14] "Lachnospiraceae UCG-001"
## [15] "Muribaculum"
## [16] "Tuzzerella"
## [17] "Candidatus Arthromitus"
## [18] "Acetatifactor"
## [19] "Marvinbryantia"
## [20] "Butyricicoccus"
## [21] "Candidatus Stoquefichus"
## [22] "Lactobacillaceae"
## [23] "Bifidobacteriaceae"
## [24] "Peptostreptococcaceae"
## [25] "Streptococcaceae"
## [26] "Prevotellaceae"
## [27] "Atopobiaceae"
## [28] "Sutterellaceae"
## [29] "Enterococcaceae"
## [30] "[Eubacterium] coprostanoligenes group"
## [31] "Erysipelatoclostridiaceae"
## [32] "Lactobacillales"
## [33] "Bifidobacteriales"
## [34] "Peptostreptococcales-Tissierellales"
## [35] "Oscillospirales"
## [36] "Burkholderiales"
## [37] "Clostridia UCG-014"
## [38] "Actinobacteria"
## [39] "Coriobacteriia"
## [40] "Gammaproteobacteria"
## [41] "Verrucomicrobiae"
## [42] "Actinobacteriota"
## [43] "Proteobacteria"
## [44] "Verrucomicrobiota"diff.corr %>%
rstatix::cor_test(vars = c(Per_Neut, Per_Eos),
vars2 = c(`Bifidobacterium`:Verrucomicrobiota),
method = "spearman") -> diff.corr.res
diff.corr.res$n_feces <- nrow(diff.meta.df)
diff.corr.res$n_mouse <- nrow(diff.meta.df)
diff.corr.res$Week <- "13"3.7 Trichrome and histopathology data
trichrome.df %>% dplyr::select(Mouse, Mean_Percent_Trichrome_Area_outliers_removed) %>%
filter(is.na(Mean_Percent_Trichrome_Area_outliers_removed) == FALSE) %>%
distinct(.keep_all = TRUE) -> trichrome.mean
hist.df %>% dplyr::select(Mouse, HE_score, PAS_score) %>%
full_join(trichrome.mean, by = "Mouse") -> hist.tri
meta.slim %>% filter(Week == 13 & Mouse %in% hist.tri$Mouse) %>%
dplyr::select(Label, Mouse) %>% left_join(hist.tri, by = "Mouse") -> hist.tri.sam
FullRA.df %>% filter(Label %in% hist.tri.sam$Label) %>%
right_join(hist.tri.sam, by = "Label") -> hist.tri.corr
hist.tri.corr %>% colnames()## [1] "Label"
## [2] "Bifidobacterium"
## [3] "Romboutsia"
## [4] "Lactococcus"
## [5] "Rikenella"
## [6] "Prevotellaceae UCG-001"
## [7] "Rikenellaceae RC9 gut group"
## [8] "Coriobacteriaceae UCG-002"
## [9] "Prevotellaceae NK3B31 group"
## [10] "Tyzzerella"
## [11] "Parasutterella"
## [12] "Lachnospiraceae UCG-001"
## [13] "Muribaculum"
## [14] "Tuzzerella"
## [15] "Candidatus Arthromitus"
## [16] "Acetatifactor"
## [17] "Marvinbryantia"
## [18] "Butyricicoccus"
## [19] "Candidatus Stoquefichus"
## [20] "Lactobacillaceae"
## [21] "Bifidobacteriaceae"
## [22] "Peptostreptococcaceae"
## [23] "Streptococcaceae"
## [24] "Prevotellaceae"
## [25] "Atopobiaceae"
## [26] "Sutterellaceae"
## [27] "Enterococcaceae"
## [28] "[Eubacterium] coprostanoligenes group"
## [29] "Erysipelatoclostridiaceae"
## [30] "Lactobacillales"
## [31] "Bifidobacteriales"
## [32] "Peptostreptococcales-Tissierellales"
## [33] "Oscillospirales"
## [34] "Burkholderiales"
## [35] "Clostridia UCG-014"
## [36] "Actinobacteria"
## [37] "Coriobacteriia"
## [38] "Gammaproteobacteria"
## [39] "Verrucomicrobiae"
## [40] "Actinobacteriota"
## [41] "Proteobacteria"
## [42] "Verrucomicrobiota"
## [43] "Mouse"
## [44] "HE_score"
## [45] "PAS_score"
## [46] "Mean_Percent_Trichrome_Area_outliers_removed"hist.tri.corr %>%
rstatix::cor_test(vars = c(HE_score:Mean_Percent_Trichrome_Area_outliers_removed),
vars2 = c("Bifidobacterium":"Verrucomicrobiota"),
method = "spearman") -> hist.corr.res
hist.corr.res$n_mouse <- nrow(hist.tri.corr)
hist.corr.res$n_feces <- nrow(hist.tri.corr)
hist.corr.res$Week <- "13"
head(hist.corr.res)4 Aggregate and correct for multiple testing
Weight.corr.res$Test <- "Weight"
glucose.corr.res$Test <- "Glucose tolerance testing"
diff.corr.res$Test <- "% immune cells; HDM"
protein.corr.res$Test <- "Serum proteins"
hist.corr.res$Test <- "Histology or % trichrome; HDM"
rbind(Weight.corr.res,
glucose.corr.res,
diff.corr.res,
protein.corr.res,
hist.corr.res) %>% adjust_pvalue(method = "BH") %>%
filter(p.adj < 0.05) %>%
add_significance() %>%
mutate(p.adj.print = format(p.adj, digits = 2)) -> micro.corr.res
f.intersect %>% dplyr::select(row, Compare_taxon) %>% distinct() -> f.intersect.taxa
micro.corr.res %>% dplyr::rename(Health_metric = var1, row = var2, Metric_Type = Test) %>%
left_join(f.intersect.taxa, by = "row") %>%
dplyr::rename(Taxonomic_Rank = Compare_taxon,
Taxon = row) %>%
dplyr::mutate(Taxonomic_Rank = factor(Taxonomic_Rank, levels = c("Phylum", "Class", "Order", "Family", "Genus"))) %>%
arrange(Taxonomic_Rank, Taxon) -> micro.corr.resf.nosurgery.intersect %>% filter(row %in% f.hfd.intersect$row)micro.corr.res %>% filter(Taxon %in% f.hfd.intersect$row)micro.corr.res %>% datatable()write_csv(micro.corr.res, file.path(git.dir, "Microbiome_corr_res.csv"), append = FALSE, col_names = TRUE)micro.corr.res %>% dplyr::count(Taxon) %>% arrange(desc(n))5 Graphs: all
f.ra %>% filter(OTU %in% f.intersect$row) %>%
dplyr::select(-Sample) %>%
dplyr::rename(taxon = OTU, RA = Abundance) %>%
mutate(Week_factor = factor(Week, levels = c("0", "10", "13")),
Diet = str_replace(Diet, "Normal_Chow", "Normal Chow"),
Diet = str_replace(Diet, "High_Fat_Diet", "High Fat Diet"),
Diet = factor(Diet, levels = c("Normal Chow", "High Fat Diet")),
Label = as.character(Label)) -> f.ra.graphf.ra.graphWeight.corr.df %>% dplyr::select(Label, Weight) %>%
right_join(f.ra.graph, by = "Label") -> f.ra.graph.corr
head(f.ra.graph.corr)corr.df %>% select(Label, AUC:Glucose_min_0) %>%
right_join(f.ra.graph.corr, by = "Label") -> f.ra.graph.corr
protein.micro.corr %>% select(Label, C_peptide_pg_ml:PYY_pg_ml) %>%
right_join(f.ra.graph.corr, by = "Label") -> f.ra.graph.corr
hist.tri.sam %>% select(Label, HE_score:Mean_Percent_Trichrome_Area_outliers_removed) %>%
right_join(f.ra.graph.corr, by = "Label") -> f.ra.graph.corr
diff.meta.df %>% select(Label, Per_Eos:Per_Neut) %>%
right_join(f.ra.graph.corr, by = "Label") -> f.ra.graph.corrhead(f.ra.graph.corr)micro.corr.res %>% filter(str_detect(Taxon, "Lactoba") == TRUE)for (i in 1:length(micro.corr.res$Health_metric)) {
yvar <- micro.corr.res$Health_metric[i]
q <- micro.corr.res$p.adj.print[i]
value <- micro.corr.res$cor[[i]]
str_glue("p = ", q, "\n Cor. coeff = ", value) -> label_corr
f.ra.graph.corr %>%
filter(taxon == micro.corr.res$Taxon[i]) %>%
ggplot(aes(x = RA, y = .data[[yvar]])) +
geom_point() +
labs(y= str_glue(micro.corr.res$Health_metric[i]),
x= str_glue(micro.corr.res$Taxon[i], " ","Relative Abundance"),
title = str_glue("Spearman's rank correlation, ", yvar,
" & ", micro.corr.res$Taxon[i])) +
theme_bw()+ expand_limits(y = 0) +
geom_text(aes(label = label_corr), x = Inf, y = Inf, vjust = "inward", hjust = "inward", family = "sans") -> p
print(p)
}## Warning: Removed 3 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 140 rows containing missing values (`geom_point()`).
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## Warning: Removed 3 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
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## Warning: Removed 140 rows containing missing values (`geom_point()`).
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## Warning: Removed 140 rows containing missing values (`geom_point()`).
## Warning: Removed 3 rows containing missing values (`geom_point()`).
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## Warning: Removed 84 rows containing missing values (`geom_point()`).
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## Warning: Removed 3 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
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## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 84 rows containing missing values (`geom_point()`).
## Warning: Removed 3 rows containing missing values (`geom_point()`).
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6 Specific taxa
Based on literature review, focus on Lachnospiraceae UCG-001, Bifidobacterium, and Parasutterella.
f.ra.graph %>%
filter(taxon == "Lachnospiraceae UCG-001" & Surgery == "None") %>% # no surgery group!!!!
ggplot(aes(x = Week_factor, y = RA)) +
geom_boxplot(width=0.2) + geom_point(size = 1) +
facet_wrap(vars(Diet)) +
labs(y="*Lachnospiraceae UCG-001* Relative Abundance", x = "Week") +
theme_bw(base_size = 14)+
theme(axis.title.y = element_markdown()) -> fig.lachno.rel
fig.lachno.rel
f.ra.graph %>%
filter(taxon == "Bifidobacterium" & Surgery == "None") %>% # no surgery group!!!!
ggplot(aes(x = Week_factor, y = RA)) +
geom_boxplot(width=0.2) + geom_point(size = 1) +
facet_wrap(vars(Diet)) +
labs(y="*Bifidobacterium* Relative Abundance", x = "Week") +
theme_bw(base_size = 14) +
theme(axis.title.y = element_markdown())-> fig.Bifido.rel
fig.Bifido.rel
f.ra.graph %>%
filter(taxon == "Parasutterella" & Surgery == "None") %>% # no surgery group!!!!
ggplot(aes(x = Week_factor, y = RA)) +
geom_boxplot(width=0.2) + geom_point(size = 1) +
facet_wrap(vars(Diet)) +
labs(y="*Parasutterella* Relative Abundance", x = "Week") +
theme_bw(base_size = 14) +
theme(axis.title.y = element_markdown()) -> fig.para.rel
fig.para.rel
micro.corr.res %>%
filter(Taxon == "Lachnospiraceae UCG-001" | Taxon == "Bifidobacterium" | Taxon == "Parasutterella") %>%
arrange(cor)protein.micro.corr %>%
ggplot(aes(x = `Lachnospiraceae UCG-001`, y = GLP1_pM)) +
geom_point() +
labs(y= "GLP-1 (pM)",
x= "*Lachnospiraceae UCG-001* Relative Abundance") +
theme_bw(base_size = 14)+ expand_limits(y = 0) +
theme(axis.title.x = element_markdown())-> fig.lachno.glp1
fig.lachno.glp1
protein.micro.corr %>%
ggplot(aes(x = Bifidobacterium, y = GLP1_pM)) +
geom_point() +
labs(y= "GLP-1 (pM)",
x= "*Bifidobacterium* Relative Abundance") +
theme_bw(base_size = 14)+ expand_limits(y = 0)+
theme(axis.title.x = element_markdown()) -> fig.bifido.glp1
fig.bifido.glp1
protein.micro.corr %>%
ggplot(aes(x = Parasutterella, y = GLP1_pM)) +
geom_point() +
labs(y= "GLP-1 (pM)",
x= "*Parasutterella* Relative Abundance") +
theme_bw(base_size = 14)+ expand_limits(y = 0) +
theme(axis.title.x = element_markdown()) -> fig.para.glp1
fig.para.glp1
plot_grid(
fig.Bifido.rel, fig.bifido.glp1,
fig.lachno.rel, fig.lachno.glp1,
fig.para.rel, fig.para.glp1,
labels = "AUTO", ncol = 2, label_size = 20, scale = 0.9,
rel_widths = c(1.3, 1)
) -> fig.corr
fig.corr
ragg::agg_jpeg(file.path(fig.dir, "fecal_corr.jpeg"), width = 12, height = 12, units = "in", res = 600)
fig.corr
dev.off()## png
## 27 Reproducibility
sessionInfo()## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] ggtext_0.1.2 cowplot_1.1.1 Hmisc_5.1-1 phyloseq_1.44.0
## [5] stringr_1.5.0 tibble_3.2.1 readr_2.1.4 tidyr_1.3.0
## [9] dplyr_1.1.3 plotly_4.10.3 DT_0.29 ggrepel_0.9.4
## [13] RColorBrewer_1.1-3 pals_1.8 ggpubr_0.6.0 ggplot2_3.4.4
## [17] rstatix_0.7.2
##
## loaded via a namespace (and not attached):
## [1] rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3
## [4] farver_2.1.1 rmarkdown_2.25 zlibbioc_1.46.0
## [7] ragg_1.2.6 vctrs_0.6.4 multtest_2.56.0
## [10] RCurl_1.98-1.13 base64enc_0.1-3 htmltools_0.5.6.1
## [13] broom_1.0.5 Rhdf5lib_1.22.1 Formula_1.2-5
## [16] rhdf5_2.44.0 sass_0.4.7 bslib_0.5.1
## [19] htmlwidgets_1.6.2 plyr_1.8.9 cachem_1.0.8
## [22] commonmark_1.9.0 igraph_1.5.1 lifecycle_1.0.3
## [25] iterators_1.0.14 pkgconfig_2.0.3 Matrix_1.6-1.1
## [28] R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [31] digest_0.6.33 colorspace_2.1-0 S4Vectors_0.38.2
## [34] textshaping_0.3.7 crosstalk_1.2.0 vegan_2.6-4
## [37] labeling_0.4.3 fansi_1.0.5 httr_1.4.7
## [40] abind_1.4-5 mgcv_1.9-0 compiler_4.3.1
## [43] bit64_4.0.5 withr_2.5.1 htmlTable_2.4.2
## [46] backports_1.4.1 carData_3.0-5 maps_3.4.1
## [49] ggsignif_0.6.4 MASS_7.3-60 biomformat_1.28.0
## [52] permute_0.9-7 tools_4.3.1 foreign_0.8-85
## [55] ape_5.7-1 nnet_7.3-19 glue_1.6.2
## [58] nlme_3.1-163 rhdf5filters_1.12.1 gridtext_0.1.5
## [61] grid_4.3.1 checkmate_2.3.0 cluster_2.1.4
## [64] reshape2_1.4.4 ade4_1.7-22 generics_0.1.3
## [67] gtable_0.3.4 tzdb_0.4.0 data.table_1.14.8
## [70] hms_1.1.3 xml2_1.3.5 car_3.1-2
## [73] utf8_1.2.4 XVector_0.40.0 BiocGenerics_0.46.0
## [76] foreach_1.5.2 pillar_1.9.0 markdown_1.11
## [79] vroom_1.6.4 splines_4.3.1 lattice_0.22-5
## [82] survival_3.5-7 bit_4.0.5 tidyselect_1.2.0
## [85] Biostrings_2.68.1 knitr_1.44 gridExtra_2.3
## [88] IRanges_2.34.1 stats4_4.3.1 xfun_0.40
## [91] Biobase_2.60.0 stringi_1.7.12 lazyeval_0.2.2
## [94] yaml_2.3.7 evaluate_0.22 codetools_0.2-19
## [97] cli_3.6.1 rpart_4.1.21 systemfonts_1.0.5
## [100] munsell_0.5.0 jquerylib_0.1.4 dichromat_2.0-0.1
## [103] Rcpp_1.0.11 GenomeInfoDb_1.36.4 mapproj_1.2.11
## [106] ellipsis_0.3.2 bitops_1.0-7 viridisLite_0.4.2
## [109] scales_1.2.1 purrr_1.0.2 crayon_1.5.2
## [112] rlang_1.1.1